General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany.
Department of Analytics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany.
Microb Physiol. 2024;34(1):1-77. doi: 10.1159/000534425. Epub 2023 Oct 10.
The denitrifying betaproteobacterium Aromatoleum aromaticum EbN1T is a facultative anaerobic degradation specialist and belongs to the environmental bacteria studied best on the proteogenomic level. This review summarizes the current state of knowledge about the anaerobic and aerobic degradation (to CO2) of 47 organic growth substrates (23 aromatic, 21 aliphatic, and 3 amino acids) as well as the modes of respiratory energy conservation (denitrification vs. O2-respiration). The constructed catabolic network is comprised of 256 genes, which occupy ∼7.5% of the coding regions of the genome. In total, 219 encoded proteins have been identified by differential proteomics, yielding a proteome coverage of ∼74% of the network. Its degradation section is composed of 31 peripheral and 4 central pathways, with several peripheral modules (e.g., for 4-ethylphenol, 2-phenylethylamine, indoleacetate, and phenylpropanoids) discovered only after the complete genome [Arch Microbiol. 2005 Jan;183(1):27-36] and a first proteomic survey [Proteomics. 2007 Jun;7(13):2222-39] of A. aromaticum EbN1T were reported. The activation of recalcitrant aromatic compounds involves a suite of biochemically intriguing reactions ranging from C-H-bond activation (e.g., ethylbenzene dehydrogenase) via carboxylation (e.g., acetophenone carboxylase) to oxidative deamination (e.g., benzylamine), reductive dearomatization (benzoyl-CoA), and epoxide-forming oxygenases (e.g., phenylacetyl-CoA). The peripheral reaction sequences are substrate-specifically induced, mediated by specific transcriptional regulators with in vivo response thresholds in the nanomolar range. While lipophilic substrates (e.g., phenolics) enter the cells via passive diffusion, polar ones require active uptake that is driven by specific transporters. Next to the protein repertoire for canonical complexes I-III, denitrification, and O2-respiration (low- and high-affinity oxidases), the genome encodes an Ndh-II, a tetrathionate reductase, two ETF:quinone oxidoreductases, and two Rnf-type complexes, broadening the electron transfer flexibility of the strain. Taken together, the detailed catabolic network presented here forms a solid basis for future systems biology-level studies with A. aromaticum EbN1T.
脱氮β-变形杆菌 Aromatoleum aromaticum EbN1T 是一种兼性厌氧降解专家，属于在蛋白质组学水平上研究得最好的环境细菌。本综述总结了目前关于 47 种有机生长基质（23 种芳香族、21 种脂肪族和 3 种氨基酸）的厌氧和需氧（至 CO2）降解以及呼吸能量保存模式（反硝化与 O2 呼吸）的知识状态。构建的代谢网络由 256 个基因组成，约占基因组编码区域的 7.5%。通过差异蛋白质组学共鉴定了 219 个编码蛋白，网络的蛋白质组覆盖率约为 74%。其降解部分由 31 个外围和 4 个中心途径组成，一些外围模块（例如，对 4-乙基苯酚、2-苯乙胺、吲哚乙酸盐和苯丙素）仅在完整基因组[Arch Microbiol. 2005 Jan;183(1):27-36]和 A. aromaticum EbN1T 的第一个蛋白质组学调查[Proteomics. 2007 Jun;7(13):2222-39]后才被发现。难降解芳香族化合物的激活涉及一系列生化上有趣的反应，范围从 C-H 键激活（例如，乙基苯脱氢酶）通过羧化（例如，苯乙酮羧化酶）到氧化脱氨（例如，苄基胺）、还原脱芳构化（苯甲酰辅酶 A）和环氧化物形成加氧酶（例如，苯乙酰辅酶 A）。外围反应序列是底物特异性诱导的，由特定的转录调节剂介导，体内响应阈值在纳摩尔范围内。疏水性底物（例如酚类）通过被动扩散进入细胞，而极性底物则需要由特定转运蛋白驱动的主动摄取。除了典型复合物 I-III、反硝化和 O2 呼吸（低亲和度和高亲和度氧化酶）的蛋白质组外，基因组还编码了一个 Ndh-II、一个四硫代盐还原酶、两个 ETF：醌氧化还原酶和两个 Rnf 型复合物，拓宽了菌株的电子传递灵活性。总的来说，这里呈现的详细代谢网络为未来使用 A. aromaticum EbN1T 进行系统生物学水平的研究奠定了坚实的基础。
